bio-alignment-msa-parsing SKILL.md skillA
bio-alignment-msa-parsing from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-alignment-msa-parsing@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-alignment-msa-parsing/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 22,084 bytes
- Repository stars
- 662
- License
- MIT
Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: BioPython 1.83+, numpy 1.26+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # MSA Parsing and Analysis Parse multiple sequence alignments to extract information, analyze content, and prepare for downstream analysis. ## Required Import **Goal:** Load modules for parsing, analyzing, and manipulating multiple sequence alignments. **Approach:** Import AlignIO for reading, Counter for column analysis, and alignment classes for constructing modified alignments. ```python from Bio import AlignIO from Bio.Align import MultipleSeqAlignment from Bio.SeqRecord import SeqRecord from Bio.Seq import Seq from collections import Counter import numpy as np import pandas as pd ``` Optional for streaming and Easel-based weighting: ```python import pyhmmer ``` ## Loading Alignments **Goal:** Read an MSA file and inspect its dimensions. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-alignment-msa-parsing@sha256:c22de96eab32dd9dThe line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_ux24yq5kcjvqqovq)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ux24yq5kcjvqqovq GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-alignment-msa-parsing GET https://markdownregistry.com/api/v1/blob/c22de96eab32dd9d9d14b2d0b323bcb982b14c0880cd739c02761056e68044f2
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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